TB-Profiler result

Run: ERR2229238
Summary

Run ID: ERR2229238

Sample name:

Date: 31-03-2023 16:51:27

Number of reads: 1110637

Percentage reads mapped: 99.14

Strain: lineage4.8

Drug-resistance: Sensitive

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491737 p.Arg319Trp missense_variant 0.13
mshA 576108 p.Ala254Gly missense_variant 0.25
mshA 576488 p.Val381His missense_variant 0.22
rpoB 760882 p.Val359Ala missense_variant 0.14
rpoC 763148 c.-222G>A upstream_gene_variant 0.12
rpoC 766746 c.3382delC frameshift_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777173 c.1308C>T synonymous_variant 0.14
mmpL5 777176 p.Glu435Asp missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472583 n.738T>G non_coding_transcript_exon_variant 0.11
rrl 1473970 n.313G>C non_coding_transcript_exon_variant 0.22
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475073 n.1416G>C non_coding_transcript_exon_variant 0.13
rrl 1476647 n.2990C>G non_coding_transcript_exon_variant 0.11
rrl 1476661 n.3004A>C non_coding_transcript_exon_variant 0.11
fabG1 1673346 c.-94C>G upstream_gene_variant 0.2
fabG1 1673349 c.-91G>C upstream_gene_variant 0.19
fabG1 1673357 c.-83G>A upstream_gene_variant 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102511 p.Ala178Thr missense_variant 0.18
PPE35 2167965 p.Ala883Gly missense_variant 0.24
PPE35 2167967 c.2646A>C synonymous_variant 0.24
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.45
PPE35 2170053 p.Thr187Ser missense_variant 0.42
PPE35 2170059 p.Val185Arg missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519022 p.Ala303Glu missense_variant 0.11
kasA 2519140 c.1026G>C synonymous_variant 0.19
kasA 2519143 c.1029G>C synonymous_variant 0.2
kasA 2519153 p.Ile347Val missense_variant 0.11
ald 3087206 c.387G>C synonymous_variant 0.12
whiB7 3568550 p.Val44Met missense_variant 0.11
Rv3236c 3612327 p.Thr264Ala missense_variant 0.11
Rv3236c 3612544 c.573T>A synonymous_variant 0.29
Rv3236c 3612671 p.Pro149Gln missense_variant 0.18
fbiB 3640818 c.-717G>A upstream_gene_variant 0.12
clpC1 4039714 p.Tyr331His missense_variant 0.12
clpC1 4040144 c.561G>C synonymous_variant 0.15
panD 4044478 c.-197G>A upstream_gene_variant 0.15
embC 4241653 c.1791C>T synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246567 c.54_55insT frameshift_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0